Merge pull request #52 from UMCUGenetics/develop

v0.4.0 Feature add contamination score

Author: ellendejong

VerifyBamID/2.0.1--h32f71e1_2/VerifyBamID2.nf

@@ -0,0 +1,32 @@
+process VerifyBamID2 {
+    tag {"VerifyBamID2 ${sample_id}"}
+    label 'VERIFYBAMID_2_0_1_h32f71e1_2'
+    label 'VERIFYBAMID_2_0_1_h32f71e1_2_VerifyBamID2'
+    container = 'quay.io/biocontainers/verifybamid2:2.0.1--h32f71e1_2'
+    shell = ['/bin/bash', '-eo', 'pipefail']
+
+    input:
+        tuple (sample_id, path(bam), path(bai))
+
+    output:
+        tuple (sample_id, path("${output_prefix}.selfSM"))
+
+    script:
+        output_prefix = "${sample_id}.contamination"
+
+        """
+        # creates a ${output_prefix}.selfSM file, a TSV file with 2 rows, 19 columns.
+        # First row are the keys (e.g., SEQ_SM, RG, FREEMIX), second row are the associated values
+        verifybamid2 \
+        --Reference ${params.genome} \
+        --BamFile ${bam} \
+        --SVDPrefix ${params.contamination_path_prefix} \
+        --UDPath ${params.contamination_sites_ud} \
+        --MeanPath ${params.contamination_sites_mu} \
+        --BedPath ${params.contamination_sites_bed} \
+        --Verbose \
+        --NumPC 4 \
+        --NumThread ${task.cpus} \
+        --Output  ${output_prefix}
+        """
+}